merge-recursive: Fix spurious 'refusing to lose untracked file...' messages

merge-recursive: Fix spurious 'refusing to lose untracked file...' messages

Calling update_stages() before update_file() can sometimes result in git
thinking the file being updated is untracked (whenever update_stages
moves it to stage 3).  Reverse the call order, and add a big comment to
update_stages to hopefully prevent others from making the same mistake.

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>